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Call for FICUS EMSL-JGI Based Research Proposals, FY 2025

Submit Letter of Intent

Timeline

Letters of intent due

Letters of intent are due at 5 p.m. PST on March 7, 2024.

The Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy (DOE) Office of Science user facility at Pacific Northwest National Laboratory, and the Joint Genome Institute (JGI), a DOE Office of Science user facility at Lawrence Berkeley National Laboratory (Berkeley Lab), are seeking collaborative research applications through the Facilities Integrating Collaborations for User Science (FICUS) program. The FICUS program was originally established in 2014 to encourage and enable ambitious multidisciplinary research projects and integrates the expertise and experimental capabilities of multiple DOE supported user facilities.  This call is supported by the Office of Science’s Biological and Environmental Research (BER) program

The fiscal year (FY) 2025 FICUS proposal call will include access to the expanded capabilities available at DOE-supported user facilities beyond JGI and EMSL, including the Bio-SANS beamline through the Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory and the Advanced Photon Source at Argonne National Laboratory through the eBERlight program. Additionally, applicants can also request access to archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites through the National Ecological Observatory Network (NEON) funded by the National Science Foundation (NSF). 

Successful applications will address high-risk/high-payoff projects in the focus topic areas that can be completed in 24 months, use a variety of available capabilities at two or more user facilities, and generate datasets beyond what users of each of these facilities can generate through separate projects. Applicants are strongly encouraged to contact facility staff (see contact information below) in advance of submitting a Letter of Intent for help with designing a set of analyses and using the capabilities at multiple user facilities that are directed at their research goals. Applicants are also encouraged to review the products of the National Microbiome Data Center (NMDC) to enable microbiome data hosting and DOE’s Systems Biology Knowledgebase (KBase) to enable both pre- and subsequent analyses of the data from their project effort.  

Focus topic areas

Proposals submitted to this call should be responsive to one or more of the following focus topic areas, which are aligned with BER.

  • Biofuels, biomaterials, and bioproducts: Proposals should be aimed at characterizing biological processes (including the pathways generated by synthetic biology approaches) that are relevant to biofuel, biomaterial, and bioproduct production and connecting these processes to omics-based analyses for DOE-relevant plants, microbes, and microbial communities including viruses. Topics of interest include the discovery, characterization, and engineering of enzymes and metabolic pathways for biomass decomposition and/or conversion to biofuels, biomaterials, and bioproducts; the utilization of C1 substrates; microbially mediated recycling and upcycling of plastics; secure biosystem design and biocontainment; genome-enabled organic and inorganic material synthesis; and investigations into organisms and/or biological products involved in plant–microbe interactions that impact biofuel and bioproduct feedstock productivity. 
  • Hydro-biogeochemistry: Proposals should seek to illuminate the key hydro-biogeochemical processes through which microorganisms influence the biogeochemical cycling and transport of key elements, nutrients, colloids, and other constituents of terrestrial ecosystems under baseline or disturbance conditions. Study systems can include soils, vegetation, microbial communities, the atmosphere, the subsurface, and land/aquatic interfaces, including but not limited to river/stream systems, coastal zones, and/or ecosystems along the rural to urban gradient. Understanding the regulatory/metabolic processes of plants, microbes, and microbial communities, including viruses, is of particular interest. Proposals should seek to link microbial populations, genes, and/or traits to molecular biogeochemistry and to the surrounding environment. 
  • Interorganismal interactions: Proposals should explore the exchange of metabolites, signaling molecules, and/or nutrients (carbon, nitrogen, and other elements) among plants, microbes, and viruses in above- and below-ground ecosystems and their interfaces (e.g., terrestrial–aquatic interfaces) and investigate signaling, cooperation, or competition via physical or chemical means under abiotic environmental stresses and perturbations (e.g., drought and salinity). Proposals focused on the impacts of biological diversity and root structure within plant populations, on plant-associated microbial communities, and on plant–microbe interactions are also encouraged. These investigations can include metabolite exchange, structural or functional characterization of transporters, surface proteins, exudates, and the enzymes, pathways, proteins, and metabolites involved in secondary metabolism that affect multiorganismal and organism–environment interactions. 
  • Novel applications of molecular techniques: Proposals should aim at multidisciplinary approaches that combine the unique capabilities at the User Facilities to make scientific advances for the DOE/BER mission. The integration of experimental and data capabilities across the scope of the user facilities and NEON would enable scientific advances integrating the expertise and experimental/technological capabilities at multiple facilities. Outcomes involve biofuels, biomaterials, biomass decomposition, bioproduct production, the use of C1 substrates, the recycling and upscaling of plastics, biocontainment, secure biosystem design, plant–microbe interactions, elemental and nutrient exchange, ecosystem resilience or plasticity in response to environmental stress or disturbances, and land–atmosphere exchanges and feedbacks. The structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., primary and secondary metabolites), or biomaterials produced by genes found in (meta)genomic data and the functional analysis of uncultivated organisms are of particular interest. For high-risk exploratory studies aimed at assessing the general feasibility or establishing proof of principle, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion. 

Highlighted Capabilities

Proposals should make use of the capabilities from two or more of the participating user facilities, where at least one of the facilities must be EMSL or JGI. 

Environmental Molecular Sciences Laboratory 

EMSL provides a wide range of unique and state-of-the-art omics, imaging, and computational capabilities that can be applied to proposals under this call. Applicants should especially consider emerging, cutting-edge capabilities that are available to users who coordinate their proposals with the EMSL scientists who lead their development. The capabilities include but are not limited to the following: 

  • New single-cell transcriptomic workflows for elucidating the intercellular signaling, communication, and ensuing heterogeneity that underpin the behavior of complex multicellular/multispecies assemblages, including microbial communities and host–microbe systems. (Contact: Alex Beliaev)
  • Developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. For example, users are sought for a recently developed probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and noncanonical amide hydrolase activity, and for developing probes for other activities. (Contact: Sankar Krishnamoorthy)
  • A stable isotope probing and analysis platform that includes labeled CO2 plant growth facilities, NMR, IRMS, and NanoSIMS. (Contacts: Mary Lipton or Pubudu Handakumbura)
  • Small sample omics analysis from a single cell or a small number of cells, detected and isolated by flow cytometry, fluorescence microscopy, and/or laser capture microdissection and enabled by microfluidics and nanoPOTS. (Contacts: Sarai Williams, James Fulcher, or Ljiljana Pasa-Tolic)
  • Spatial metabolomics, used to investigate the spatial distribution of molecules within biological samples. (Contacts: Chris Anderton, Dusan Velickovic, and Kristin Burnum-Johnson)
  • Structural biology approaches utilizing cell-free expression, native mass spectrometry, and NMR capabilities for the characterization of protein complexes. (Contact: Irina El Khoury)
  • Cryo-TEM for the atomic-resolution structural analysis of proteins, protein complexes, and/or small molecule crystals or for the high-resolution tomographic analysis of whole cells and tissues. (Contacts: James Evans, Irina El Khoury, or Amar Parvate)
  • Cryo-FIB/SEM for site-selective sample preparation for cryo-EM/tomography or the serial section slice-and-view 3-D imaging of large tissue or plant/microbe interactions. (Contacts: James Evans or Trevor Moser) See capability for more information. 
  • A tender X-ray nanotomography system for the 3-D nanoscale imaging of cells and biological materials. (Contacts: James Evans or Scott Lea)
  • High mass-resolution soil organic matter composition analysis using Fourier-Transform Ion Cyclotron Resonance (FTICR) mass spectrometry. (Contact: Will Kew)
  • Mass spectrometry for top-down (intact) proteomics, with access to capabilities including 21-tesla FTICR MS. (Contact: Ljiljana Pasa-Tolic)
  • Mass spectrometry for bottom-up (fragmented) proteomics using three main approaches of quantitative analysis: label-free, isobaric labeling, and targeted. (Contact: Mary Lipton)
  • Mass spectrometry for the identification and quantification of conventional targeted and untargeted metabolomics and lipidomics. (Contact: Chaevien Clendinen)
  • A micro-X-ray computed tomography system for the characterization of biogeochemical samples such as soil, rhizosphere, and sediment samples to investigate the porous microstructure, plant root architecture, hydrology, etc. Two resolution options are available: 0.8 and 0.2 µm. (Contact: Tamas Varga)
  • Atom probe tomography to analyze the compositional interface and characterize the microstructure of bioorganic–mineral interfaces and chemical gradients in biological systems. (Contact: Danny Perea)
  • Transmission electron microscopy, scanning electron microscopy, and helium ion microscopy for chemical and morphological analyses of colloids, organo-mineral associations, and nanominerals. (Contact: Odeta Qafoku)
  • Mössbauer spectroscopy for the analysis of nano-Fe minerals and Fe–organic matter assemblages. (Contact: Ravi Kukkadapu)
  • A noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth media. (Contact: Amir Ahkami or Thomas Wietsma)
  • Optical coherence tomography for a noninvasive approach for the in situ, 3-D imaging of living tissues. The approach can be applied to static samples or deployed in various growth chambers to provide time-series imaging of plants or other systems. (Contact: Amir Ahkami)
  • Liquid- and solid-state NMR-based metabolomics to define the metabolite profile in a biological system, including the primary and secondary metabolites and plant cell wall components. See capability for more information.  (Contacts: David Hoyt and Andrew Lipton)
  • Interactive data visualization tools that support the exploration of complex natural organic matter or proteomics data and the comparison of data across treatment groups . (Contacts: Satish Karra and Kelly Stratton)
  • Tahoma, BER’s heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs. See capability for more information. (Contact: Satish Karra
  • A suite of TerraForms platforms to measure the impact of target soil parameters on ecological interactions, including pore-scale micromodels, mineral-amended TerraForms, RhizoChip, and Bioprinted Synthetic Soil Aggregates. These TerraForms platforms are ideal for multiomics characterization and the multimodal imaging of the spatial organization of soil and rhizosphere communities (plant, bacteria, and fungi) and mapping the molecular exchanges between organisms. (Contacts: Amir Ahkami, Arunima Bhattacharjee, and Jayde Aufrecht)
  • NanoSIMS analysis, which enables the imaging of trace elements and isotope ratios with a high resolution (50 nm) and sensitivity (ppm). Ideally suited for observing the fate of added isotopically enriched compounds in plant–microbe–soil systems. (Contact: Jeremy Bougoure)

Learn more about these and other EMSL capabilities. 

Joint Genome Institute 

JGI employs both next-generation short-read sequencing platforms and 3rd-generation single-molecule/long-read capabilities as well as DNA synthesis and mass-spectrometry-based metabolomics. The capabilities available for this call are listed below; more details about JGI products, including the expected cycle times, are also available. FICUS proposals should request no more than 3 Tb of sequencing, 500 kb of synthesis, and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Requests for Pacific Biosciences long-read sequencing are capped at 1 Tb and 50 samples (up to 200 samples for bacterial/archaeal isolate genomes). Requests for DAP-seq should include a minimum of 92 transcription factors. For EcoFAB experiments, up to 50 EcoFABs are available. Researchers are encouraged to review JGI’s sample submission guidelines to obtain additional information about the amounts of material that are required for various product types. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals. Successful projects frequently exploit a combination of capabilities. 

  • De novo sequencing and annotation of plant, algal, fungal, bacterial, archaeal, and viral genomes 
  • Resequencing for variation detection 
  • Fluorescence-activated cell sorting for targeted metagenomics and single-cell genomics 
  • Microbial and/or viral community DNA/RNA sequencing and annotation (i.e., metagenomes and metatranscriptomes) 
  • Stable-isotope-probing-enabled metagenomics 
  • Transcriptome analysis including coding transcript annotation and expression profiling 
  • Prokaryotic whole genome DNA methylation analysis 
  • Transcription factor binding site discovery with DAP-seq 
  • Gene and pathway DNA synthesis 
  • Whole genome gRNA library construction and QC 
  • Organism engineering 
  • LC-MS/MS-based metabolomic and exometabolomic analysis of polar (e.g., amino acids, organic acids, sugars, nucleobases, etc.) and nonpolar metabolites (e.g., secondary metabolites, lipids, etc.) 
  • Integrated metabolomic and genomic analyses 
  • Investigations using EcoFAB devices and, if desired, a defined microbiome supplied by JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes. 

For general questions, please contact Christa Pennacchio, Project Management Office. For questions about the appropriateness of projects or experimental design, please contact Tanja Woyke, Deputy for User Programs. Technical and Scientific Leads will also be available to answer any questions prior to proposal submission. 

Center for Structural Molecular Biology 

CSMB supports the user access and science program of the Biological Small-Angle Neutron Scattering (Bio-SANS) instrument at the High-Flux Isotope Reactor located at Oak Ridge National Laboratory. Neutrons provide unique structural information due to their sensitivity to hydrogen and deuterium that is unattainable by other means. Through this FICUS partnership, CSMB is providing access to the resources listed below for studies of hierarchical and complex biological systems. 

  • Small-angle neutron scattering at Bio-SANS, which provides structural information about a range of biological systems across length scales from 1 to 100 nm. Examples include biomacromolecules and their complexes in solution, biomembranes, and hierarchical and complex systems such as plant cell walls and soils. 
  • Deuterium labeling of biological macromolecules including proteins, lipids, nucleic acids, and other biopolymers. 

These tools help researchers understand how macromolecular systems are formed and how they interact with other systems in living cells. For further information about CSMB and Bio-SANS please visit https://www.ornl.gov/facility/csmb, and/or contact Hugh O’Neill). 

Advanced Photon Source  

The Advanced Photon Source (APS) at Argonne National Laboratory (ANL) is being upgraded with new transformative accelerator technology. A new design for the storage ring, the beamline improvement program, and the new feature beamlines will offer a wide range of X-ray-based tools that will provide novel opportunities for research pertinent to the BER mission, including biological, geological, geochemical, and environmental sciences, to address existing and new scientific challenges. The eBERlight program is a virtual Collaborative Access Team (CAT) at APS. It will serve as a liaison between the user community pursuing research within the BER mission and the APS after the upgrade. The eBERlight program offers an integrated platform for enhancing user science through focused communication with users and coordinated activities among the relevant APS beamlines. 

In addition to APS X-ray beamlines and techniques, eBERlight will offer expertise and additional infrastructure available at ANL that includes (i) the Advanced Protein Characterization Facility (APCF, sector 84 of APS, sample preparation), (ii) the Advanced Leadership Computing Facility (ALCF, exascale computing for data processing using supercomputers), (iii) the APS cryolab (sample preparation), and (iv) Molecular Environmental Science and Biogeochemical Process Group (MESBPG) laboratories (sample preparation). 

Specific capabilities/resources include 

  • Protein production and structural characterization resources/services in the Advanced Protein Characterization Facility for gene cloning, recombinant protein expression, purification, characterization, and crystallization (access to the lab to perform the work or mail-in service for the gene-to-structure pipeline). 
  • Macromolecular crystallography for the determination of the 3-D structures of macromolecules: proteins, nucleic acids, and their complexes. 
  • Full-field X-ray imaging for micro- and nano-X-ray computed tomography (CT) to enable the 3-D visualization of soil cores or aggregates, plant structures, etc. The sample size ranges from micrometers to centimeters. 
  • Scanning X-ray microscopy for the visualization of elemental distributions [X-ray fluorescence (XRF) in two and/or three dimensions and structural information (ptychography) in two and/or three dimensions]. XRF approaches are applicable for the mapping of elements with an atomic number of 13 (aluminum) and higher; ptychography is a computational scanning microscopy technique for acquiring structural information with a resolution beyond the limits of X-ray optics. Both techniques can be applied to a variety of samples in both biological and environmental research, such as soils, plants, the rhizosphere, aerosol particles, and microorganisms. The sample size for XRF ranges from micrometers to centimeters with a spatial resolution ranging from 5 nm to 30 µm. The highest achievable spatial resolution for ptychography is 5 nm. 

For general questions, please contact Karolina Michalska. For specific questions about APS capabilities, contact Zou Finfrock

National Ecological Observatory Network  

NEON, a large facility project funded by the NSF, is a continental-scale platform for ecological research. It comprises terrestrial, aquatic, atmospheric, and remote sensing measurements and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. In addition to its openly available data products, NEON provides access to hundreds of thousands of archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites. The NEON infrastructure is geographically distributed across the United States and will generate data for ecological research over a 30-year period. The network is designed to enable the research community to ask and address their own questions on a regional to continental scale around a variety of environmental challenges. Requests for large numbers of samples or that require additional sample processing may incur a service fee. Additional information about the network is available below: 

 For general questions, please contact Michael SanClements

Data Policies: 

The data generated from user projects are subjected to the data policies of the relevant facility. For more details, see the following links: 

Applicants are encouraged to interface with the National Microbiome Data Collaborative (NMDC) for the registration and processing of their data and the Department of Energy’s Systems Biology Knowledgebase (KBase) for advanced analysis and data integration. 

NMDC is an integrated microbiome data ecosystem hosting high-quality, consistently processed multiomics microbiome data to enable data sharing, management, and cross-comparison across studies in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Applicants interested in collaborating with the NMDC team and having their data hosted within the NMDC Data Portal should indicate so in their proposal (Contact: Emiley Eloe-Fadrosh; eaeloefadrosh@lbl.gov). 

KBase is a free, open-source data analysis platform for system biology research that supports the FAIR data principles, reproducible analysis workflows, and the sharing and publishing of datasets and the knowledge generated from research efforts and analyses. Analyses supported by KBase are available at http://www.kbase.us/learn. Applicants are encouraged to reach out to the KBase staff to discuss how they can support your project (Contact: Elisha Wood-Charlson; emwood-charlson@lbl.gov). 

Submission Steps

Partnering User Facilities

Joint Genome Institute

The mission of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility of Lawrence Berkeley National Laboratory (Berkeley Lab) and part of the Biosciences Area, is to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, JGI unites the expertise at Berkeley Lab, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. Located in the Integrative Genomics Building in the heart of the Berkeley Lab campus, atop the hills above Berkeley, California, the JGI is operated by the University of California for the U.S. Department of Energy. JGI provides integrated high-throughput sequencing, DNA design and synthesis, metabolomics and computational analysis that enable systems-based scientific approaches to these challenges.

JGI Contacts

Center for Structural Molecular Biology

The Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory is an open access user program dedicated to advancing instrumentation and methods for determining the three-dimensional structures of biomacromolecules and their assemblies as well as hierarchical structures and biomimetic systems.

CSMB Contacts

Advanced Photon Source

Description

The Advanced Photon Source at Argonne National Laboratory is a storage-ring-based high-energy X-ray light source facility. It is one of five X-ray light sources owned and funded by the U.S. Department of Energy Office of Science. The APS began operation on March 26, 1995.

Review criteria

FICUS proposals are reviewed for technical feasibility by scientific staff at each facility that is called out in the proposal. Proposals also undergo external peer review against four scientific criteria. For each criterion, the reviewers rate the proposals as Extraordinary, Excellent, Good, Fair, or Poor and provide detailed comments on the quality of the proposals to support their rating, specifically noting the proposals’ strengths and weaknesses. Reviewers also provide overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for the Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to the facilities’ management. 

Criterion 1: Scientific merit and quality of the proposed research (25%) 

Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? 

Criterion 2: Qualifications of the proposed research team to achieve the proposal goals and contribute to high-impact science (25%) 

Potential Considerations: Does the proposal team, combined with relevant staff expertise from the appropriate facilities, possess the appropriate breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)? The size and productivity of the user community will also be considered. 

Note: Impact factors are a measure of the average number of citations per published article. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field. 

Criterion 3: Relevance of the proposed research to DOE’s missions (25%) 

Potential Considerations: What is the relationship of the proposed research to DOE’s and BER’s missions? Does the research project significantly advance the mission goals? Proof of concept proposals for the demonstration of a technology that would be applicable to a DOE and/or BER mission are acceptable. How well does the project plan represent a unique or innovative demonstration, and to what extent does it advance the mission area? 

Criterion 4: Appropriateness and reasonableness of the request for resources for the proposed research (25%) 

Potential Considerations: Are the capabilities requested from at least two institutions essential to performing this research, and is one of those either EMSL or JGI? Does the project generate a dataset unique to these facilities and beyond what each could generate by itself? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project? Is the specified work plan practical and achievable within the specified project timeframe (e.g., shorter than JGI’s CSP projects)?